Leber, R. | bioRxiv Science

bioRxiv2024

k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance

BackgroundWheat landraces and cultivars stored in gene banks worldwide represent a valuable source of genetic diversity for discovering genes critical for agriculture, which is increasingly constrained by climate change and inputs reduction. We assembled and genotyped, using DArTseq technology, a panel of 461 accessions representative of the genetic diversity of Swiss wheat material. The collection was evaluated for powdery mildew resistance under field conditions for two consecutive years and at the seedling stage with 10 different wheat powdery mildew isolates. ResultsTo identify the genetic basis of mildew resistance in wheat, we developed a k-mer-based GWAS approach using multiple fully-assembled genomes including Triticum aestivum as well as four progenitor genomes. Compared to approaches based on single reference genomes, we unambiguously mapped an additional 25% resistance-associated k-mers. Our approach outperformed SNP-based GWAS in terms of number of loci identified and precision of mapping. In total, we detected 34 (Pm) powdery mildew resistance loci, including seven previously-described and more importantly 27 novel loci active at the seedling stage. Furthermore, we identified a region associated with adult plant resistance, which was not detected with SNP-based approaches. ConclusionsThe described non-reference-based approach highlights the potential of integrating multiple wheat reference genomes with k-mer GWAS to harness the untapped genetic diversity present in germplasm collections.

genomics↗

bioRxiv2023

A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance

Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies. Key MessageA bread wheat panel reveals rich genetic diversity in Turkish, Pakistani, and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies.

plant biology↗